diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 53 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ace30bdbd1..4ae1ad0470 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2534,6 +2534,59 @@ subsequent visualization, annotation and storage of results.") ;; LGPLv2.1+ (license (list license:gpl2 license:lgpl2.1+)))) +(define-public smithlab-cpp + (let ((revision "1") + (commit "728a097")) + (package + (name "smithlab-cpp") + (version (string-append "0." revision "." commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74")))) + (build-system gnu-build-system) + (arguments + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:tests? #f ;no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-samtools-headers + (lambda _ + (substitute* '("SAM.cpp" + "SAM.hpp") + (("sam.h") "samtools/sam.h")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (include (string-append out "/include/smithlab-cpp"))) + (mkdir-p lib) + (mkdir-p include) + (for-each (cut install-file <> lib) + (find-files "." "\\.o$")) + (for-each (cut install-file <> include) + (find-files "." "\\.hpp$"))) + #t)) + (delete 'configure)))) + (inputs + `(("samtools" ,samtools-0.1) + ("zlib" ,zlib))) + (home-page "https://github.com/smithlabcode/smithlab_cpp") + (synopsis "C++ helper library for functions used in Smith lab projects") + (description + "Smithlab CPP is a C++ library that includes functions used in many of +the Smith lab bioinformatics projects, such as a wrapper around Samtools data +structures, classes for genomic regions, mapped sequencing reads, etc.") + (license license:gpl3+)))) + (define-public preseq (package (name "preseq") |